Hepatitis B virus (HBV) infection seems to be related to gut microbiota. This study aims to explore the effects of HBV infection on gut microbiota and possible immunological mechanisms using the Chinese woodchuck model. Nine adult woodchucks were randomly divided into Cyclosporine A (CsA) or Control group. Animals were orally treated with CsA and saline for 2 weeks before WHV inoculation, and continued until 8 weeks after that. Blood CsA concentrations were tested at 2 weeks after administration and before discontinuation. Quantitative PCR was used to detect serum WHV DNA. Flow cytometry was used to detect T cell immune response. Feces were collected for 16S rRNA sequencing. The result shows CsA oral administration can reach effective blood drug concentration in woodchucks and successfully prolong WHV replication. After 2 weeks of oral treatment, there was no significant difference in the gut microbiota between the two groups. At the clearance period of serum WHV, the relative abundance of Prevotella and Prevotella genera in the phylum Bacteroidetes significantly increased, while the relative abundance of Firmicutes significantly decreased. Meanwhile, the CD107a degranulation of CD4-T cells in peripheral blood showed a decreasing trend, while there was no significant difference in the frequency of PD-1+ CD4-T cells. In Conclusion, oral administration of CsA can significantly prolong the replication time of WHV in Chinese woodchucks. The gut microbiota of Chinese woodchuck undergoes significant changes during serum WHV clearance, which implies the Chinese woodchuck model can be used to study the interaction between HBV infection and gut microbiota.